I need to add a certifcate to my key store so that I can securely connect to our LDAP server. I'm using Java 1.6 but I can't find any file with an extension ".jks" in my JAVA_HOME. If I need to create one, how do I then register it with the Java runtime environment?
You need to add the certificate to your truststore. There are several options on how to do this including adding it to the system wide cacerts or jssecacerts file. Look at the JSSE reference guide for all the details.